Molecular dynamics simulation and EPR spectroscopy of nitroxide side chains in bacteriorhodopsin

A novel approach for the simulation of electron paramagnetic resonance (EPR ) spectra was used to combine molecular dynamics (MD) simulations with expe rimental data. Reorientational dynamics trajectories of a sequence of nitro xide side chains attached to cysteine substitution mutants of bacteriorhodo psin (BR) were calculated by means of MD simulations. EPR spectra calculate d from these data were found to be in excellent agreement with the experime ntal spectra. Simulation of EPR difference spectra for two BR conformations reveal that experimentally detected changes of the nitroxide dynamics duri ng the catalytic cycle of BR are consistent with a transient conformational change of helix F. (C) 2000 Elsevier Science B.V. All rights reserved.